[Rdkit-discuss] reading multiple conformers from file

[Thomas E. <te...@gm...>]

Hello everyone,

I am a new user of RDkit and I was looking in the documentation for an easy
way to load multiple conformers from a structure file like .sdf. The code
must 1) distinguish between different protonation states of the same
molecule,  2) create a new Mol() object for each protonation state and load
into it the respective conformers.

Apparently I can work out a solution for 1)
using mol.GetProp('_Name'), mol.GetNumAtoms, mol.GetNumBonds and other
properties, but I was wondering if there is any more straight forward way
to do it.
For 2) I guess I must iterate over all molecules in the input file, create
new Mol() objects (one for each protonation state of each ligand) and add
conformers to these new Mol() objects. Again this sounds easily
programmable, but sounds like a very common operation, thus I was wondering
if it has been implemented in a function.

thanks in advance
Thomas


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Thomas Evangelidis

Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic

email: te...@ph...

          te...@gm...


website: https://sites.google.com/site/thomasevangelidishomepage/